Comments on "clock"

I recently read
Rhythms of Life,
a book about
circadian rhythms.
I was very struck by (the currently most plausible guess at) the
underlying cell-level mechanism.

It's a negative feedback system, like a pendulum (which, as it
swings higher, also feels a stronger force pulling it back towards
the central position). Startling thing number 1: one crucial step
in the feedback loop is DNA transcription. I'd always
vaguely assumed that, roughly speaking, the instructions in a
cell's DNA determine how the cell is "built" and are more or less
passive thereafter (readers who actually know some biology,
please feel free to laugh at me at this point), but no.

Here's a simplified description of how it works: there are two
proteins (call them A and B), described by genes
a and b. Protein B promotes the expression
of gene a, but protein A attaches to protein B
and stops it doing this. So, the more A we have, the less A gets made;
if the details of how this works out are right, we get the sort of
negative feedback loop required to produce an oscillation.

Startling thing number 2 is how easily this produces entrainment
to the light/dark cycle. It turns out that A is degraded
by exposure to light, and this is enough. (Which shouldn't have
been surprising, since in general oscillators very easily get
entrained to anything in their environment, but it surprised me
anyway.)

So: suppose we have a stable 24-hour-ish cycle, and then
it becomes light earlier than "expected". Then A gets
degraded more rapidly, at around the time when it would have
been being degraded anyway, and so the cycle is a bit shorter.
Similarly if the onset of light is later than expected. If the
light period goes on for longer than expected, then again
A gets degraded faster -- but now at a time when
its quantity should be beginning to ramp up; so the cycle
becomes longer. And so forth.

Three caveats. Firstly, this is all oversimplified; for
instance, A and B are actually pairs of
proteins that work together, and there are other mechanisms
involved in, e.g., arranging for the period of the oscillator
not to be much too fast. Secondly, strictly it only applies to
fruit flies, and the corresponding systems in other organisms
aren't so well understood. Thirdly, lots of important details
(for instance, how the period of the clock manages to be largely
insensitive to temperature, when chemical reactions consistently
run faster at higher termperatures) are still unknown.

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